# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Nov 17 13:06:08 2022
#   Inital geometry file: a 41 line input string
#   Ligand name: (phosphonooxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CO[P](O)(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PGA  PGA  "2-PHOSPHOGLYCOLIC ACID"  ligand  14  9  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PGA
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PGA  P     P  P     0   1.310   8.1388  -1.8939  18.4765
 PGA  O1P   O  O2    0  -0.553   8.1098  -1.5513  16.9143
 PGA  O2P   O  O     0  -0.647   9.3271  -1.4180  19.2066
 PGA  O3P   O  OH1   0  -0.635   7.9011  -3.4712  18.4593
 PGA  O4P   O  OH1   0  -0.714   6.7212  -1.3458  18.9477
 PGA  C2    C  CH2   0  -0.284   9.2765  -1.6886  16.1227
 PGA  C1    C  C     0   0.513   9.0409  -2.5629  14.9127
 PGA  O1    O  O     0  -0.481   9.8875  -2.6976  14.0671
 PGA  O2    O  OH1   0  -0.564   7.8584  -3.1437  14.8964
 PGA  HOP3  H  HOH1  0   0.526   8.1075  -3.9096  19.2965
 PGA  HOP4  H  HOH1  0   0.464   6.7147  -0.4097  19.1901
 PGA  H21   H  HCH2  0   0.252   9.5885  -0.7014  15.7761
 PGA  H22   H  HCH2  0   0.318  10.1209  -2.1150  16.6727
 PGA  HO2   H  HOH1  0   0.497   7.7717  -3.7007  14.1067

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PGA  P    O1P   single  1.600  0.020  1.600
 PGA  P    O2P   double  1.474  0.020  1.474
 PGA  P    O3P   single  1.595  0.020  1.595
 PGA  P    O4P   single  1.591  0.020  1.591
 PGA  O1P  C2    single  1.417  0.020  1.417
 PGA  O3P  HOP3  single  0.850  0.020  0.980
 PGA  O4P  HOP4  single  0.850  0.020  0.980
 PGA  C2   C1    single  1.511  0.020  1.511
 PGA  C2   H21   single  0.970  0.020  1.090
 PGA  C2   H22   single  0.970  0.020  1.090
 PGA  C1   O1    double  1.204  0.020  1.204
 PGA  C1   O2    single  1.318  0.020  1.318
 PGA  O2   HO2   single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PGA  O4P   P    O3P  102.19  3.000
 PGA  O4P   P    O2P  117.41  3.000
 PGA  O3P   P    O2P  116.41  3.000
 PGA  O4P   P    O1P  101.49  3.000
 PGA  O3P   P    O1P  101.45  3.000
 PGA  O2P   P    O1P  115.42  3.000
 PGA  C2    O1P  P    120.67  3.000
 PGA  HOP3  O3P  P    114.02  3.000
 PGA  HOP4  O4P  P    114.44  3.000
 PGA  H22   C2   H21  106.94  3.000
 PGA  H22   C2   C1   107.30  3.000
 PGA  H21   C2   C1   108.27  3.000
 PGA  H22   C2   O1P  113.11  3.000
 PGA  H21   C2   O1P  108.97  3.000
 PGA  C1    C2   O1P  112.03  3.000
 PGA  O2    C1   O1   124.96  3.000
 PGA  O2    C1   C2   113.88  3.000
 PGA  O1    C1   C2   121.15  3.000
 PGA  HO2   O2   C1   110.08  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PGA  CONST_01  HO2  O2   C1   C2    180.00   0.0  0
 PGA  CONST_02  HO2  O2   C1   O1      0.00   0.0  0
 PGA  Var_01    C1   C2   O1P  P     126.08  30.0  3
 PGA  Var_02    O1   C1   C2   O1P   173.56  30.0  3
 PGA  Var_03    O2   C1   C2   O1P    -6.95  30.0  3
 PGA  Var_04    C2   O1P  P    O2P    42.26  30.0  3
 PGA  Var_05    C2   O1P  P    O3P   -84.52  30.0  3
 PGA  Var_06    C2   O1P  P    O4P   170.35  30.0  3
 PGA  Var_07    H21  C2   O1P  P    -114.15  30.0  3
 PGA  Var_08    H22  C2   O1P  P       4.65  30.0  3
 PGA  Var_09    H21  C2   C1   O1     53.37  30.0  2
 PGA  Var_10    H22  C2   C1   O1    -61.73  30.0  2
 PGA  Var_11    H21  C2   C1   O2   -127.14  30.0  2
 PGA  Var_12    H22  C2   C1   O2    117.76  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PGA  plan-1  C2   0.020
 PGA  plan-1  C1   0.020
 PGA  plan-1  O1   0.020
 PGA  plan-1  O2   0.020
 PGA  plan-1  HO2  0.020

